Modified oligonucleotides and applications thereof

ABSTRACT

Disclosed, among other things, are primers containing certain modified nucleobases in the 3′ terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 11/250,192, filed Oct. 12, 2005, which is a continuation of U.S. patent application Ser. No. 11/106,021, filed Apr. 14, 2005, now abandoned, which claims a priority benefit under 35 U.S.C. §119(e) from U.S. Patent Application No. 60/562,388, filed Apr. 14, 2004, which is incorporated herein by reference.

The present teachings relate to nucleic acid amplification, for example, compounds and methods for application in the polymerase chain reaction (PCR).

Detecting the presence of target nucleic acids plays an important role in a variety for applications in diverse fields, including: medical diagnostics, forensic science and genetic analysis. PCR is an example of a nucleic acid amplification method that can provide a highly sensitive means for detecting the presence of target nucleic acids by selective amplification of a target nucleic acid sequence.

A significant problem with nucleic acid amplifications such as PCR is the generation of non-specific amplification products. One example of a non-specific amplification process that can be problematic in PCR reactions is “primer-dimer” amplification. Primer-dimer amplification can result when, for example, the 3′ terminal region of a primer has some degree of complimentarity with itself or another primer. Such primers can hybridize to one another to form primer-dimers. Amplification of the primer-dimer can then lead to primer-dimer amplicons that can in turn act as templates for further amplification. One outcome of such a process being a depletion of primers resulting in reduced sensitivity or even a failure to amplify the intended target nucleic acid.

To complicate the problem, the addition of a large excess of primers during PCR reactions allows even weak complimentarity at the 3′ terminal region to result in primer-dimer amplicons. As a result there is a need to develop reagents and methods that suppress primer-dimer formation in amplification reactions such as PCR.

It has now been found that, surprisingly, incorporation of certain modified nucleobases in the 3′ terminal region of primers can significantly reduce the formation of primer-dimer amplicons during amplification reactions.

In some embodiments, the present teachings provide polynucleotides comprising at least one modified purine nucleobase of the structure

wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, azido, nitro, cyano, unsubstituted or substituted amino, C₁-C₆ alkyl, C₁-C₆ alkynyl, C₁-C₆ substituted alkynyl, unsubstituted or substituted phenylalkynyl, and unsubstituted or substituted aryl, or R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, C₁-C₆ alkyl, C₁-C₆ alkynyl, and C₁-C₆ substituted alkynyl, such that at least one said modified purine nucleobase is no more than 3 nucleotides from the 3′ terminus of the primer. In some embodiments, polynucleotides of the present invention are extendable at the 3′-end. In some embodiments, at least one said modified purine nucleobase comprises the structure

In some embodiments, at least one said modified purine nucleobase is no more than 2 nucleotides from the 3′ terminus of the polynucleotide. In some embodiments, at least one said modified purine nucleobase is no more than 1 nucleotide from the 3′ terminus of the polynucleotide. In some embodiments, at least one said modified purine nucleobase is the 3′ terminal nucleobase of the polynucleotide. In some embodiments, polynucleotides of the present teachings can be polynucleotide primers. In some embodiments, polynucleotide primers of the present teachings can include at least one of a detectable label, a quencher or a minor groove binder, or a combination thereof.

In some embodiments, the present teachings provide for methods of primer extension comprising, annealing a polynucleotide primer to a denatured DNA template such that, the polynucleotide primer anneals to a complementary polynucleotide sequence on a strand of the denatured DNA template to form a primer-template complex, and extending the primer portion of the primer-template complex to form a double stranded amplicon, wherein the polynucleotide primer is a primer according to the present teachings.

In some embodiments, the present teachings provide for methods of primer extension comprising, after the step of extending, denaturing the double stranded amplicon. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least one time. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 10 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 20 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 30 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 40 times.

In some embodiments, the present teachings provide for methods of primer extension, wherein the extending takes place in the presence of extendable nucleotide triphosphates and non-extendable nucleotide triphosphates to form DNA amplicon fragments. In some embodiments the method of primer extension comprises, detecting the DNA amplicon fragments.

In some embodiments, the present teachings provide methods of primer extension comprising: i) annealing a first polynucleotide primer and a second polynucleotide primer to a first and second strand of a denatured DNA template such that, the first polynucleotide primer anneals to a complementary oligonucleotide sequence on the first strand of the denatured DNA template and the second polynucleotide primer anneals to a complementary oligonucleotide sequence on the second strand of the denatured DNA template to form a first and a second primer-template complex, and ii) extending the primer portion of at least one of the first and second primer-template complex to form double stranded DNA amplicon, where at least one of the first polynucleotide primer or the second polynucleotide primer can be a polynucleotide according to the present teachings.

In some embodiments, the present teachings provide methods of primer extension comprising, prior to the step of annealing, forming a mixture comprising a first polynucleotide primer, a second polynucleotide primer, a DNA template, and other primer extension reagents. In some embodiments, the present teachings provide methods of primer extension comprising, after the step of forming but prior to the step of annealing, denaturing the DNA template to form a first strand of denatured DNA template and a second denatured DNA template. In some embodiments, the present teachings provide methods of primer extension comprising, after the step of extending, denaturing the double stranded DNA amplicon.

In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can optionally be repeated from 1-100 times. Optionally, the steps of annealing, extending and denaturing the double stranded DNA amplicon can be repeated from 1-50 times. It will be understood that the present teachings encompass all possible ranges for repeating the steps of annealing, extending and denaturing the double stranded DNA amplicon between 1 and 100 times. That is, the steps of annealing, extending and denaturing the double stranded DNA amplicon can be repeated from 1 time up to 100 times and any number of times in between. For example, the range, of 1-10 will be understood to include all possible ranges using all integers between 1 and 10, i.e.-1, 2, 3, 4, 5, 6, 7, 8, 9, 10. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can optionally be repeated greater than 1 time. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can optionally be repeated greater than 10 times. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can optionally be repeated greater than 20 times. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can optionally be repeated greater than 30 times. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can optionally be repeated greater than 40 times. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can optionally be repeated greater than 50 times.

In some embodiments, the present teachings provide for methods of primer extension comprising, prior to the step of extending the primer portion, annealing a polynucleotide probe to a first or second strand of a denatured DNA template such that, the polynucleotide probe anneals to a complementary polynucleotide sequence on the first strand of the denatured DNA template and/or the polynucleotide probe anneals to a complementary oligonucleotide sequence on the second strand of the denatured DNA template. In some embodiments, the polynucleotide probe comprises at least one detectable label. In some embodiments, the polynucleotide probe further comprises at least one of a quencher, a minor groove binder or both. In some embodiments, the polynucleotide probe can be a polynucleotide of the present teachings.

In some embodiments, the present teachings provide methods of oligonucleotide ligation comprising, i) forming a complex comprising a first and a second polynucleotide strand annealed to a DNA template such that, the first polynucleotide strand anneals to a first complementary polynucleotide sequence on the strand of the denatured DNA template and the second polynucleotide strand anneals to a second complementary polynucleotide sequence on the strand of the denatured DNA template, wherein the second complementary polynucleotide sequence on the strand of the denatured DNA template is located 5′ to the first complementary polynucleotide sequence on the strand of the denatured DNA template, and ii) forming a stable covalent bond between the first and second polynucleotide strands, wherein at least one of the first polynucleotide strand or the second polynucleotide strand is a polynucleotide of the present teachings.

In some embodiments, the present teachings provide for methods for detecting a target polynucleotide sequence comprising, (a) reacting a target polynucleotide strand with a first probe pair comprising (i) a first polynucleotide probe containing a sequence that is complementary to a first target region in the target strand and (ii) a second polynucleotide probe comprising a sequence that is complementary to a second target region in the target strand, wherein the second region is located 5′ to the first region and overlaps the first region by at least one nucleotide base, under conditions effective for the first and second probes to hybridize to the first and second regions in the target strand, respectively, forming a first hybridization complex, (b) cleaving the second probe in the first hybridization complex, to form a second hybridization complex comprising the target strand, the first probe, and a first fragment of the second probe having a 5′ terminal nucleotide located immediately contiguous to a 3′ terminal nucleotide of the first probe, (c) ligating the first probe to the hybridized fragment of the second probe to form a first ligated strand hybridized to the target strand, (d) denaturing the first ligated strand from the target strand, and (e) performing one or more additional cycles of steps (a) through (d), with the proviso that in the last cycle, step (d) is optionally omitted, wherein at least one of the first probe, the second probe or both is a polynucleotide comprising at least one modified purine nucleobase comprising the structure

wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, azido, nitro, cyano, unsubstituted or substituted amino, C₁-C₆ alkyl, C₁-C₆ alkynyl, C₁-C₆ substituted alkynyl, unsubstituted or substituted phenylalkynyl, and unsubstituted or substituted aryl, or wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, C₁-C₆ alkyl, C₁-C₆ alkynyl, and C₁-C₆ substituted alkynyl, such that at least one said modified purine nucleobase is no more than 3 nucleotides from the 3′ terminus of the first polynucleotide probe or the second polynucleotide probe or both, and the first polynucleotide probe is extendable at its 3′-end. In some embodiments, at least one said modified purine nucleobase comprises the structure

In some embodiments, at least one said modified purine nucleobase is no more than 2 nucleotides from the 3′ terminus of the first polynucleotide probe, the second polynucleotide probe or both. In some embodiments, at least one said modified purine nucleobase is no more than 1 nucleotides from the 3′ terminus of the first polynucleotide probe, the second polynucleotide probe or both. In some embodiments, the modified purine nucleobase is the 3′ terminal nucleotide of the first polynucleotide probe, the second polynucleotide probe or both.

In some embodiments, the first polynucleotide probe, the second polynucleotide probe or both comprise at least one of a detectable label, a quencher or a minor groove binder, or any combination thereof. In some embodiments, the first region overlaps the second region by one nucleotide base. In some embodiments, the 5′ end of the first probe terminates with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 5′ end of the first probe terminates with a nucleotide 5′ hydroxyl group. In some embodiments, the 5′ end of the second probe terminates with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 5′ end of the second probe terminates with a nucleotide 5′ hydroxyl group. In some embodiments, the 3′ end of the second probe terminates with a group other than a nucleotide 3′ hydroxyl group. In some embodiments, the 3′ end of the second probe terminates with a nucleotide 3′ phosphate group.

In some embodiments, the present teachings provide methods for detecting a target polynucleotide sequence comprising, (a) reacting a target-complementary strand with a second probe pair comprising (i) a third polynucleotide probe containing a sequence that is complementary to a first region in the target-complementary strand and (ii) a fourth polynucleotide probe containing a sequence that is complementary to a second region in the target-complementary strand, wherein the second region is located 5′ to the first region and overlaps the first region by at least one nucleotide base, under conditions effective for the for the third and fourth probes to hybridize to the first and second regions in the target-complementary strand, respectively, forming a third hybridization complex, (b) cleaving the fourth probe in the second hybridization complex, to form a forth hybridization complex comprising the target-complementary strand, the third probe, and a first fragment of the forth probe having a 5′ terminal nucleotide located immediately contiguous to a 3′ terminal nucleotide of the third probe, (c) ligating the third probe to the hybridized fragment of the fourth probe to form a second ligated strand hybridized to the target-complementary strand, (d) denaturing the second ligated strand from the target-complementary strand, and (e) performing one or more additional cycles of steps (a) through (d), with the proviso that in the last cycle, step (d) is optionally omitted. In some embodiments, at least one of the third probe or the forth probe or both is a polynucleotide comprising at least one modified purine nucleobase comprising the structure

wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, azido, nitro, cyano, unsubstituted or substituted amino, C₁-C₆ alkyl, C₁-C₆ alkynyl, C₁-C₆ substituted alkynyl, unsubstituted or substituted phenylalkynyl, and unsubstituted or substituted aryl, or wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, C₁-C₆ alkyl, C₁-C₆ alkynyl, and C₁-C₆ substituted alkynyl, such that at least one said modified purine nucleobase is no more than 3 nucleotides from the 3′ terminus of the third probe or the forth probe or both, and the third polynucleotide probe is extendable at its 3′-end. In some embodiments, at least one said modified purine nucleobase comprises the structure

In some embodiments, at least one said modified purine nucleobase is no more than 2 nucleotides from the 3′ terminus of the first polynucleotide probe, the second polynucleotide probe or both. In some embodiments, at least one said modified purine nucleobase is no more than 1 nucleotide from the 3′ terminus of the first polynucleotide probe, the second polynucleotide probe or both. In some embodiments, said modified purine nucleobase can be the 3′ terminal nucleotide of the first polynucleotide probe, the second polynucleotide probe or both. In some embodiments, the first polynucleotide probe, the second polynucleotide probe or both can comprise at least one of a detectable label, a quencher or a minor groove binder, or any combination thereof. In some embodiments, the 5′ end of the third probe optionally terminates with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 5′ end of the third probe optionally terminates with a nucleotide 5′ hydroxyl group. In some embodiments, the 5′ end of the fourth probe optionally terminates with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 5′ end of the fourth probe optionally terminates with a nucleotide 5′ hydroxyl group. In some embodiments, the 5′ ends of the first, second, third and fourth probes optionally terminate with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 3′ end of the fourth probe optionally terminates with a group other than a nucleotide 3′ hydroxyl group. In some embodiments, the 3′ end of the fourth probe optionally terminates with a nucleotide 3′ phosphate group. In some embodiments, at least one of the probes contains a detectable label. In some embodiments, the label can be a fluorescent label. In some embodiments, the label can be a radiolabel. In some embodiments, the label can be a chemiluminescent label. In some embodiments, the label can be an enzyme. In some embodiments, at least one of the first probe and the third probe contains a detectable label. In some embodiments, each of the first probe and third probe contains a detectable label. In some embodiments, the detectable labels on the first probe and third probe are the same. In some embodiments, at least one of the second probe and the fourth probe contains a detectable label. In some embodiments, each of the second probe and the fourth probe contains a detectable label. In some embodiments, the second probe and fourth probe contain the same detectable label. In some embodiments, said cleaving produces a second fragment from the second probe which does not associate with the second hybridization complex, and the method further includes detecting said second fragment from the second probe. In some embodiments, said cleaving produces a second fragment from the forth probe which does not associate with the forth hybridization complex, and the method further includes detecting said second fragment from the forth probe. In some embodiments, at least one of the second probe and the fourth probe contains both (i) a fluorescent dye and (ii) a quencher dye which is capable of quenching fluorescence emission from the fluorescent dye when the fluorescent dye is subjected to fluorescence excitation energy, and said cleaving severs a covalent linkage between the fluorescent dye and the quencher dye in the second probe and/or fourth probe, thereby increasing an observable fluorescence signal from the fluorescent dye. In some embodiments, the second probe and the fourth probe each contain (i) a fluorescent dye and (ii) a quencher dye.

In some embodiments, methods of the present teachings for detecting target polynucleotide sequences method further include detecting both second fragments. In some embodiments, the second fragment comprises one or more contiguous nucleotides substantially non-complementary to the target strand. In some embodiments, the one or more contiguous nucleotides comprise 1 to 20 nucleotides.

In some embodiments, methods of the present teachings for detecting target polynucleotide sequences further include immobilizing the second fragment on a solid support. In some embodiments, methods of the present teachings for detecting target polynucleotide sequences further include subjecting the second fragment to electrophoresis. In some embodiments, methods of the present teachings for detecting target polynucleotide sequences further include detecting the second fragment by mass spectrometry. In some embodiments, methods of the present teachings for detecting target polynucleotide sequences comprise detecting the second fragment after the last cycle. In some embodiments, methods of the present teachings for detecting target polynucleotide sequences comprise detecting the second fragment during or after a plurality of cycles. In some embodiments, methods of the present teachings for detecting target polynucleotide sequences comprise detecting the second fragment during all of the cycles.

In some embodiments, methods of the present teachings for detecting target polynucleotide sequences further include detecting the first hybridization complex, the second hybridization complex, or both, after at least one cycle. In some embodiments, the method further includes detecting the third hybridization complex, the fourth hybridization complex, or both, after at least one cycle. In some embodiments, the method further includes detecting the first ligated strand, the second ligated strand, or both, after at least one cycle. In some embodiments, the detecting comprises an electrophoretic separation step.

In some embodiments, the present teachings provide for methods of fragment analysis comprising: i) annealing an oligonucleotide primer to a denatured DNA template such that, the oligonucleotide primer anneals to a complementary oligonucleotide sequence on a strand of the denatured DNA template to form a primer-template complex, ii) extending the primer portion of the primer-template complex in the presence of deoxyribonucleic acids and non-extendable ribonucleic acids to form DNA amplicon fragments, and iii) detecting the DNA amplicon fragments, where the oligonucleotide primer is an polynucleotide of the present teachings.

Scheme 1 below illustrates an exemplary polynucleotide comprising a plurality, (x), of nucleotides, “N”, that may define a desired nucleotide sequence, wherein the subscripts 1, 2, 3 . . . x refer to the position of the nucleotide in the primer relative to the 3′ end, and “ . . . ” indicates the possibility of one or more additional nucleotides between N_(x) and N₇.

5′-N_(x) . . . N₇N₆N₅N₄N₃N₂N₁-3′  Scheme 1

Thus, N₁ is located at the 3′ terminus of the exemplary polynucleotide, and can be referred to as the 3′ terminal nucleotide of the exemplary polynucleotide. Similarly, N₂ is located at the second nucleotide position, and can be referred to as being 1 nucleotide from the 3′ terminus. Similarly, N₃ is located at the third nucleotide position, and can be referred to as being 2 nucleotides from the 3′ terminus. Similarly, N₄ is located at the fourth nucleotide position, and can be referred to as being 3 nucleotides from the 3′ terminus. It is believed that the effect of reduced primer-dimer formation that results from incorporation of nucleobases of the present teachings into primers will decrease in primers having no nucleotide of the present teachings any nearer the 3′-terminus than about the N₄ position.

As used herein, the terms oligonucleotide, polynucleotide and nucleic acid are used interchangeably to refer to single- or double-stranded polymers of DNA, RNA or both including polymers containing modified or non-naturally occurring nucleotides. In addition, the terms oligonucleotide, polynucleotide and nucleic acid refer to any other type of polymer comprising a backbone and a plurality of nucleobases that can form a duplex with a complimentary polynucleotide strand by nucleobase-specific base-pairing. including, but not limited to, peptide nucleic acids (PNAs) which are disclosed in, for example, Nielsen et al., Science 254:1497-1500 (1991), bicyclo DNA oligomers (Bolli et al., Nucleic Acids Res. 24:4660-4667 (1996)) and related structures.

In some embodiments, polynucleotides of the present teachings can comprise a backbone of naturally occurring sugar or glycosidic moieties, for example, β-D-ribofuranose. In addition, in some embodiments, modified nucleotides of the present teachings can comprise a backbone that includes one or more “sugar analogs”. As used herein, the term “sugar analog” refers to analogs of the sugar ribose. Exemplary ribose sugar analogs include, but are not limited to, substituted or unsubstituted furanoses having more or fewer than 5 ring atoms, e.g., erythroses and hexoses and substituted or unsubstituted 3-6 carbon acyclic sugars. Typical substituted furanoses and acyclic sugars are those in which one or more of the carbon atoms are substituted with one or more of the same or different —R, —OR, —NRR or halogen groups, where each R is independently —H, (C₁-C₆) alkyl or (C₃-C₁₄) aryl. Examples of unsubstituted and substituted furanoses having 5 ring atoms include but are not limited to 2′-deoxyribose, 2′-(C₁-C₆)-alkylribose, 2′-(C₁-C₆)-alkoxyribose, 2′-(C₅-C₁₄)-aryloxyribose, 2′,3′-dideoxyribose, 2′,3′-dideoxy-ribose, 2′-deoxy-3′-haloribose, 2′-deoxy-3′-fluororibose, 2′-deoxy-3′-chlororibose, 2′-de-oxy-3′-aminoribose, 2′-deoxy-3′-(C₁-C₆)-alkylribose, 2′-deoxy-3′-(C₁-C₆)-alkoxyribose, 2′-deoxy-3′-(C₅-C₁₄), 3′-(C₁-C₆)-aryloxyribose alkylribose-5′-triphosphate, 2′-deoxy-3′-(C₁-C₆)-alkylribose-5′-triphosphate, 2′-deoxy-3′-(C₅-C₁₄) 2′-deoxy-3′-(C₁-C₆)-alkoxyribose-5′-triphosphate, -aryl-oxyribose-5′-triphosphate, 2′-deoxy-3′-haloribose-5′-triphosphate, 2′-deoxy-3′-aminoribose-5′-triphosphate, 2′,3′-dideoxyribose-5′-triphosphate or 2′,3′-dide-hydroribose-5′-triphosphate. Further sugar analogs include but are not limited to, for example “locked nucleic acids” (LNAs), i.e., those that contain, for example, a methylene bridge between C-4′ and an oxygen atom at C-2′, such as

that are described in Wengel, et al. WO 99/14226, incorporated herein by reference, and Wengel J., Acc. Chem. Res., 32:301-310 (1998).

In some embodiments, polynucleotides of the present teachings include those in which the phosphate backbone comprises one or more “phosphate analogs”. The term “phosphate analog” refers to analogs of phosphate wherein the phosphorous atom is in the +5 oxidation state and one or more of the oxygen atoms are replaced with a non-oxygen moiety. Exemplary analogs include, but are not limited to, phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate, phosphoramidate, boronophosphates, and associated counterions, including but not limited to H⁺, NH₄ ⁺, Na⁺, Mg⁺⁺ if such counterions are present. Polynucleotides of the present teachings containing phosphate analogs can comprise, for example, phosphorothioate linkages, methylphosphonates and/or phosphoroamidates (see, Chen et al., Nucl Acids Res., 23:2662-2668 (1995)). Combinations of polynucleotide linkages are also within the scope of the present teachings.

In some embodiments, polynucleotides described herein can be incorporated into PNA and DNA/PNA chimeras. Including, peptide nucleic acids (PNAs, also known as polyamide nucleic acids), see, for example, Nielsen et al., Science 254:1497-1500 (1991). PNAs contain heterocyclic nucleobase units that are linked by a polyamide backbone instead of the sugar-phosphate backbone characteristic of DNA and RNA. PNAs are capable of hybridization to complementary DNA and RNA target sequences. Synthesis of PNA oligomers and reactive monomers used in the synthesis of PNA oligomers are described in, for example, U.S. Pat. Nos. 5,539,082; 5,714,331; 5,773,571; 5,736,336 and 5,766,855. Alternate approaches to PNA and DNA/PNA chimera synthesis and monomers for PNA synthesis have been summarized in, for example, Uhlmann, et al., Angew. Chem. Int. Ed. 37:2796-2823 (1998).

In some embodiments, polynucleotides of the present teachings can range in size from a few nucleotide monomers in length, e.g. from 5 to 80, to hundreds or thousands of nucleotide monomers in length. For example, polynucleotides of the present teachings can contain from 5 to 50 nucleotides, 5 to 30 nucleotides, or 5 to 20 nucleotides. When, in some embodiments, polynucleotides of the present teachings contain, for example, from 5 to 30 nucleotides, such a range includes all possible ranges of integers between 5 and 30, for example 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 an 30 nucleotides in length. Whenever a polynucleotide is represented by a sequence of letters, such as “ATGCCTG,” it will be understood that the nucleotides are in 5′ to 3′ order from left to right and that “A” denotes deoxyadenosine, “C” denotes deoxycytidine, “G” denotes deoxyguanosine, and T denotes thymidine, unless otherwise indicated. Additionally, whenever a polynucleotide of the present teachings is represented by a sequence of letters that includes an “X”, it will be understood that the “X” denotes a variable nucleotide monomer, where “X” is a nucleotide monomer other than “A”, “C”, “G” or “T”.

In some embodiments, polynucleotides of the present teachings can serve as primers in amplification reactions. As used herein, “primer” refers to a polynucleotide as defined herein having a 3′ terminus that is extendable by addition of one or more nucleotide monomers or by ligation of a ligation probe.

In some embodiments, the present teachings provide for polynucleotide primers comprising at least one nucleotide having a nucleobase of the structure

wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, C₁-C₆ alkyl, C₁-C₆ alkynyl, and C₁-C₆ substituted alkynyl, at least one said modified purine nucleobase is no more than 3 nucleotides from the 3′ terminus and the polynucleotide primer is extendable at the 3′-end.

As used herein, “substituted” as in “substituted alkynyl” means that the moiety that is substituted (e.g., alkynyl moiety) comprises one or more non-hydrogen substituents. Such substituents include, but are not limited to, —F, —Cl, —Br, —CF₃, amine, —OH, —CCl₃, —CN, —CHO, —CO₂R, —SO₃R, —PO₃RR, —C(O)NRR and —NO₂ where R can be any of —H, C₁-C₆ alkyl or C₃-C₁₀ aryl.

As used herein, “alkyl” refers to a saturated or unsaturated, branched, straight-chain or cyclic monovalent hydrocarbon radical derived by the removal of one hydrogen atom from a single carbon atom of a parent alkane, alkene or alkyne. Typical alkyl groups include, but are not limited to, methyl (methanyl); ethyls such as ethanyl, ethenyl, ethynyl; propyls such as propan-1-yl, propan-2-yl (isopropyl), cyclopropan-1-yl, prop-1-en-1-yl, prop-1-en-2-yl, prop-2-en-1-yl, cycloprop-1-en-1-yl; cyclo-prop-2-en-1-yl, prop-1-yn-1-yl , prop-2-yn-1-yl, etc.; butyls such as butan-1-yl, butan-2-yl (sec-butyl), 2-methyl-propan-1-yl (isobutyl), 2-methyl-propan-2-yl (t-butyl), cyclobutan-1-yl, but-1-en-1-yl, but-1-en-2-yl, 2-methyl-prop-1-en-1-yl, but-2-en-1-yl , but-2-en-2-yl, buta-1,3-dien-1-yl, buta-1,3-dien-2-yl, cyclobut-1-en-1-yl, cyclo-but-1-en-3-yl, cyclobuta-1,3-dien-1-yl, but-1-yn-1-yl, but-1-yn-3-yl, but-3-yn-1-yl, etc.; and the like.

As used herein, “alkyl diradical” refers to an alkyl group wherein a second hydrogen atom has been removed from a second carbon atom of a parent alkane, alkene or alkyne.

As used herein, “aryl” refers to a monovalent aromatic hydrocarbon radical derived by the removal of one hydrogen atom from a single carbon atom of an aromatic ring system. Typical aryl groups include, but are not limited to, radicals derived from aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, chrysene, coronene, fluoranthene, fluorene, hexacene, hexaphene, hexylene, as-indacene, s-indacene, indane, indene, naphthalene, octacene, octaphene, octalene, ovalene, penta-2,4-diene, pentacene, pentalene, pentaphene, perylene, phenalene, phenanthrene, picene, pleiadene, pyrene, pyranthrene, rubicene, triphenylene, trinaphthalene, and the like. In some embodiments, the aryl group is (C₅-C₂₀) aryl or (C₅-C₁₀) aryl. Further aryl groups are phenyl (C₆ aryl) and naphthyl (C₁₀ aryl).

As used herein, unsubstituted amino means NH₂, and substituted amino means mono or di-substituted amino of the form NR_(a)R_(b), wherein R_(a) and R_(b) are each separately selected from —H, C₁-C₆ alkyl, substituted C₁-C₆ alkyl, or together are C₁-C₆ alkyl diradical chain or substituted C₁-C₆ alkyl diradical chain. In some embodiments, compounds of the invention contain substituted amino selected from dimethylamino and diethylamino.

As used herein, “unsubstituted phenylalkynyl” refers to PhC/C—, and “substituted phenylalkynyl” refers to phenylalkynyl containing one or more substituents as described above.

As used herein, “nucleotide” refers to naturally occurring nucleotides having naturally occurring nucleobases as well as non-naturally occurring nucleotides that comprise monomer units corresponding to the polynucleotides described above and/or a “modified nucleobase”. As used herein, the term “modified nucleobase” includes nucleobases that differ from the naturally-occurring bases (e.g. A, G, C, T and U) by addition and/or deletion of one or more functional groups, differences in the heterocyclic ring structure (i.e., substitution of carbon for a heteroatom, or vice versa), capable of nucleobase-specific base-pairing with naturally occurring nucleobases. Examples of modified nucleotides are those based on a pyrimidine structure or a purine structure, with the former including, for example, 5-substituted pyrimidines and the latter including, for example, 7-deazapurines and their derivatives and pyrazolopyrimidines (see PCT WO 90/14353 and U.S. Pat. No. 6,127,121).

Further examples of modified nucleobases include, but are not limited to, 6-amino-3-prop-1-ynyl-5-hydropyrazolo[3,4-d]pyrimidin-4-one (PPPG), 6-amino-3-(3-hydroxyprop-1-ynyl)-5-hydropyrazolo[3,4-d]pyrimidin-4-one (HOPPPG), 6-amino-3-(3-aminoprop-1-ynyl)-5-hydropyrazolo[3,4-d]pyrimidin-4-one (NH₂PPPG), 4-amino-3-(prop-1-ynyl)pyrazolo[3,4-d]pyrimidine (PPPA), 4-amino-3-(3-hydroxyprop-1-ynyl)-pyr-azolo[3,4-d]-pyrimidine (HO-PPPA), 4-amino-3-(3-aminoprop-1-ynyl)pyrazolo[3,4-d]-pyrimidine (NH₂PPPA), 3-prop-1-ynylpyrazolo[3,4-d]pyrimidin-4,6-diamine ((NH₂)₂— PPPA), 2-(4,6-diaminopyrazolo[3,4-d]pyrimidin-3-yl)ethyn-1-ol ((NH₂)₂PPPAOH), 3-(2-aminoethynyl)-pyrazolo[3,4-d]pyrimidin-4,6-diamine ((NH₂)₂PPPANH2), 5-[4-amino-3-(3-methoxyprop-1-ynyl)pyrazol[3,4-d]pyrimidinyl]-2-(hydroxymethyl)oxolan-3-ol (CH₃OPPPA), 6-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-(3-methoxy-prop-1-ynyl)-5-hydropyrazolo[3,4-d]pyrimidin-4-one (CH₃OPPPG), 4-(4,6-diamino-1H-pyrazolo[3,4-d]pyrimidin-3-yl)but-3-yn-1-ol (Super A), 6-amino-3-(4-hydroxybut-1-ynyl)-1,5-dihydropyrazolo[3,4-d]pyrimidin-4-one, 3-iodo-1H-pyrazolo[3,4-d]pyrimidin-4,6-diamine ((NH₂)₂PPAI), 3-bromo-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine ((NH₂)₂—PPABr), 3-chloro-1H-pyrazolo[3,4-d]pyrimidin-4,6-diamine ((NH₂)₂PPACl), 3-iodo-1H-pyrazolo-[3,4-d]pyramidin-4-ylamine (PPAI), 3-bromo-1H-pyrazolo[3,4-d]pyrimidin-4-ylamine (PPABr), 3-chloro-1H-pyrazolo[3,4-d]pyrimidin-4-ylamine (PPACl), 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one (ppG or PPG, also known as Super G) and 4-amino-1H-pyrazolo[3,4-d]pyrimidine (ppA or PPA).

All tautomeric forms of naturally occurring bases, modified bases and base analogues may be included in oligonucleotides of the present teachings.

Accordingly, any combination of normal bases, unsubstituted pyrazolo[3,4-d]pyrimidine bases (e.g., PPG and PPA), 3-substituted pyrazolo[3,4-d]pyrimidines, modified purines, modified pyrimidines, universal bases, sugar modifications, or backbone modification of a DNA, PNA or DNA/PNA chimera are within the scope of the present teachings.

As used herein, modified nucleotides do not encompass those wherein the nucleobase has been modified by attachment of a blocking and/or protecting group to an exocyclic nitrogen atom or to an endocyclic nitrogen atom (i.e. —a nitrogen within the nucleobase ring) such that the ability of the nucleotide to form a stable hydrogen bond is disrupted or eliminated by the presence of the protecting group or blocking group, see, for example, Will, S. C., et al. U.S. Pat. No. 6,001,611.

In some embodiments oligonucleotides of the present teachings can be conjugated to at least one detectable label, nonfluorescent quencher and/or at least one stabilizing moiety. In some embodiments oligonucleotides of the present teachings that are conjugated to at least one detectable label, nonfluorescent quencher and/or at least one stabilizing moiety can serve as probes or primers.

The term “detectable label” refers to any moiety that, when attached to oligonucleotides of the present teachings, render such oligonucleotides detectable using known detection means. Exemplary detectable labels include, but are not limited to, fluorophores, chromophores, radioisotopes, spin-labels, enzyme labels or chemiluminescent labels that allow for direct detection of a labeled compound by a suitable detector, or a binding pair, for example, a ligand, such as an antigen or biotin, that can bind specifically with high affinity to a detectable anti-ligand, such as a labeled antibody or avidin. In some embodiments the labels can be fluorescent dyes, such as fluorescein or rhodamine dyes or fluorescent dye pairs, such as FRET dyes.

In some embodiments, polynucleotides of the present teachings can comprise one or more “nonfluorescent quencher” moieties. As used herein, “nonfluorescent quencher” includes but is not limited to, for example, particular azo dyes (such as DABCYL or DABSYL dyes and their structural analogs), triarylmethane dyes such as malachite green or phenol red, 4′,5′-diether substituted fluoresceins (U.S. Pat. No. 4,318,846), asymmetric cyanine dye quenchers (see, Lee et al., U.S. Pat. No. 6,080,868 and Lee, et al., U.S. Pat. No. 6,348,596), or nonfluorescent derivatives of 3- and/or 6-amino xanthene that is substituted at one or more amino nitrogen atoms by an aromatic or heteroaromatic ring system (Haugland, et al., U.S. Pat. No. 6,399,392).

“Nonfluorescent”, as used herein, indicates that the fluorescence efficiency of the quenching moiety in an assay solution as described for any of the methods herein is less than or equal to 5 percent emission at emission-λ_(max). In some embodiments, less than or equal to 1 percent emission at emission-λ_(max). In some embodiments of the present teachings, the covalently bound quenching moiety exhibits a quantum yield of less than about 0.1 percent emission at emission-λ_(max). In some embodiments, less than about 0.01 percent emission at emission-λ_(max).

In some embodiments, polynucleotides of the present teachings can be conjugated to at least one “stabilizing moiety”. As used herein, the term “stabilizing moiety” refers to moieties that include but are not limited to minor groove binder (MGB) moieties. A variety of suitable minor groove binders have been described in the literature. See, for example, Kutyavin, et al. U.S. Pat. No. 5,801,155; Wemmer, D. E., and Dervan P. B., Current Opinion in Structural Biology, 7:355-361 (1997); Walker, W. L., Kopka, J. L. and Goodsell, D. S., Biopolymers, 44:323-334 (1997); Zimmer, C & Wahnert, U. Prog. Biophys. Molec. Bio. 47:31-112 (1986) and Reddy, B. S. P., Dondhi, S. M., and Lown, J. W., Pharmacol. Therap., 84:1-111 (1999).

Suitable methods for attaching MGBs (as well as reporter groups such as fluorophores and quenchers described above) through linkers to polynucleotides are described in, for example, U.S. Pat. Nos. 5,512,677; 5,419,966; 5,696,251; 5,585,481; 5,942,610 and 5,736,626. Minor groove binders include, for example, the trimer of 3-carbamoyl-1,2-dihydro-(3-H7)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI₃) and the pentamer of N-methylpyrrole-4-carbox-2-amide (MPC₅). Additional MGB moieties are disclosed in U.S. Pat. No. 5,801,155. In certain embodiments, the MGBs can have attached water solubility-enhancing groups (e.g., sugars or amino acids).

Polynucleotides of the present teachings can find use as primers and/or probes in, for example, polynucleotide chain extension or ligation reactions. As used herein, “chain extension reaction” refers to primer extension reactions in which at least one polynucleotide of the present teachings (e.g. —as primers or ligation probes) can be annealed to at least one DNA template strand. After the step of annealing in a polynucleotide chain extension reaction, the primer can then be extended by at least one nucleotide to form an amplicon or extension product. Alternatively, after the step of annealing in a polynucleotide chain extension reaction, the primer can be ligated to a second ligation probe to form a ligation product. The present teachings encompass all possible chain extension reactions including, but not limited to, polymerase chain reaction (PCR), nested PCR, asynchronous PCR, real time PCR, TaqMan assays, DNA sequencing, cycled DNA sequencing, oligonucleotide ligation assay (OLA), and fragment analysis, described in, for example, The PCR Technique: DNA Sequencing II, Eaton Publishing Co. (1997), Genome Analysis, A Laboratory Manual Volume 1: Analyzing DNA, Birren, B., Green, E., Klapholz, S., Myers, R. M. and Roskams, J. Eds., Cold Spring Harbor Laboratory Press (1997), Innis, M. et al., PCR Protocols: A Guide to Methods and Applications, Academic Press (1989), Chen, C. et al., U.S. Patent Application Pub. No. 2003/0207266 A1, Erlich, et al., U.S. Pat. No. 5,314,809, U.S. Pat. No. 6,221,606 and Bi, W., et al., U.S. Pat. No. 6,511,810. Oligonucleotides of the present teachings can be used in any of the above primer extension reactions as either primers or probes where each is appropriate.

In some embodiments, the present teachings provide for methods of primer extension comprising, annealing a polynucleotide primer to a denatured DNA template such that, the polynucleotide primer anneals to a complementary polynucleotide sequence on a strand of the denatured DNA template to form a primer-template complex, and extending the primer portion of the primer-template complex to form a double stranded amplicon, wherein the polynucleotide primer is a primer according to the present teachings.

In some embodiments, the present teachings provide for methods of primer extension comprising, after the step of extending, denaturing the double stranded amplicon. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least one time. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 10 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 20 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 30 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 40 times.

In some embodiments, the present teachings provide for a method of primer extension comprising i) annealing a first polynucleotide primer and a second polynucleotide primer to a first and second strand of a denatured DNA template such that, the first polynucleotide primer anneals to a complementary oligonucleotide sequence on the first strand of the denatured DNA template and the second polynucleotide primer anneals to a complementary oligonucleotide sequence on the second strand of the denatured DNA template to form a first and a second primer-template complex, and ii) extending the primer portion of at least one of the first and second primer-template complex to form double stranded DNA amplicon, wherein at least one of the first polynucleotide primer or the second polynucleotide primer can be a polynucleotide of the present teachings. In some embodiments, prior to the step of annealing, the method can include the step of forming a mixture comprising a first polynucleotide primer, a second polynucleotide primer, a DNA template, and other primer extension reagents, including, for example buffers and polymerases. In some embodiments, polymerases for use in the present teachings can comprise at least one thermostable polymerase, including, but not limited to, Taq, Pfu, Vent, Deep Vent, Pwo, UITma, and Tth polymerase and enzymatically active mutants and variants thereof. Such polymerases are well known and/or are commercially available. Descriptions of polymerases can be found, among other places, at the world wide web URL: the-scientist.library.upenn.edu/yr1998/jan/profile1_(—)980105.html.

In some embodiments, after the step of forming but prior to the step of annealing, the method can include the step of denaturing the DNA template to form a first strand of denatured DNA template and a second denatured DNA template. In some embodiments, after the step of extending, denaturing the double stranded DNA amplicon. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can be repeated from 1-100 times. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can be repeated from 10-100 times. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can be repeated from 20-100 times. In some embodiments, the steps of annealing, extending and denaturing the double stranded DNA amplicon can be repeated from 30-100 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least one time. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 10 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 20 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 30 times. In some embodiments, the steps of annealing, extending and denaturing can be repeated at least 40 times.

In some embodiments, the present teachings provide for methods of primer extension comprising, prior to the step of extending the primer portion, annealing a polynucleotide probe to a first or second strand of a denatured DNA template such that, the polynucleotide probe anneals to a complementary polynucleotide sequence on the first strand of the denatured DNA template and/or the polynucleotide probe anneals to a complementary oligonucleotide sequence on the second strand of the denatured DNA template. In some embodiments, the polynucleotide probe comprises at least one detectable label. In some embodiments, the polynucleotide probe further comprises at least one of a quencher, a minor groove binder or both. In some embodiments, the polynucleotide probe can be a polynucleotide of the present teachings.

In some embodiments, the present teachings provide “fragment analysis” or “genetic analysis” methods, wherein labeled polynucleotide fragments can be generated through template-directed enzymatic synthesis using labeled primers or nucleotides, the fragments can be subjected to a size-dependent separation process, e.g., electrophoresis or chromatography; and, the separated fragments can be detected subsequent to the separation, e.g., by laser-induced fluorescence. In some embodiments, multiple classes of polynucleotides are separated simultaneously and the different classes are distinguished by spectrally resolvable labels.

In some embodiments, the present teachings provide a method of fragment analysis in which fragment classes can be identified and defined in terms of terminal nucleotides so that a correspondence is established between the four possible terminal bases and the members of a set of spectrally resolvable dyes. Such sets are readily assembled from the fluorescent dyes known in the art by measuring emission and absorption bandwidths using commercially available spectrophotometers. In some embodiments, fragment classes are formed through chain termination methods of DNA sequencing, i.e., dideoxy DNA sequencing, or Sanger-type sequencing.

Sanger-type sequencing involves the synthesis of a DNA strand by a DNA polymerase in vitro using a single-stranded or double-stranded DNA template whose sequence is to be determined. Synthesis is initiated at a defined site based on where an oligonucleotide primer anneals to the template. The synthesis reaction is terminated by incorporation of a nucleotide analog that will not support continued DNA elongation. Exemplary chain-terminating nucleotide analogs include the 2′,3′-dideoxynucleoside 5′-triphosphates (ddNTPs) which lack the 3′-OH group necessary for 3′ to 5′ DNA chain elongation. When proper proportions of dNTPs (2′-deoxynucleoside 5′-triphosphates) and one of the four ddNTPs are used, enzyme-catalyzed polymerization will be terminated in a fraction of the population of chains at each site where the ddNTP is incorporated. If labeled primers or labeled ddNTPs are used for each reaction, the sequence information can be detected by fluorescence after separation by high-resolution electrophoresis. In the chain termination method, dyes of the invention can be attached to either sequencing primers or dideoxynucleotides. In the method, fluorescent dye molecules can be linked to a complementary functionality at, for example, the 5′-terminus of a primer, e.g. following the teaching in Fung, et al., U.S. Pat. No. 4,757,141; on the nucleobase of a primer; or on the nucleobase of a dideoxynucleotide, e.g. via the alkynylamino linking groups disclosed by Hobbs et al, in European Patent Application No. 87305844.0, and Hobbs et al., J. Org. Chem., 54: 3420 (1989) incorporated herein by reference.

In some embodiments, labeled polynucleotides can be preferably separated by electrophoretic procedures as disclosed in, for example, Rickwood and Hames, Eds., Gel Electrophoresis of Nucleic Acids: A Practical Approach, IRL Press Limited, London, 1981; Osterman, Methods of Protein and Nucleic Acid Research, Vol. 1 Springer-Verlag, Berlin, 1984; or U.S. Pat. Nos. 5,374,527, 5,624,800 and/or 5,552,028. In some embodiments, the type of electrophoretic matrix can be crosslinked or uncrosslinked polyacrylamide having a concentration (weight to volume) of between about 2-20 weight percent. In some embodiments, the polyacrylamide concentration is between about 4-8 percent. In some embodiments, for example in DNA sequencing, the electrophoresis matrix can include a denaturing agent, e.g., urea, formamide, and the like. Detailed procedures for constructing such matrices are given by, for example, Maniatis et al., “Fractionation of Low Molecular Weight DNA and RNA in Polyacrylamide Gels Containing 98% Formamide or 7 M Urea,” in Methods in Enzymology, 65: 299-305 (1980); Maniatis et al., “Chain Length Determination of Small Double- and Single-Stranded DNA Molecules by Polyacrylamide Gel Electrophoresis,” Biochemistry, 14: 3787-3794 (1975); Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, pgs. 179-185 (1982); and ABI PRISM™ 377 DNA Sequencer User's Manual, Rev. A, January 1995, Chapter 2 (Applied Biosystems, Foster City, Calif.). It will be understood that optimal electrophoresis conditions, for example, polymer concentration, pH, temperature, and concentration of denaturing agent, employed in a particular separation depends on many factors, including the size range of the nucleic acids to be separated, their base compositions, whether they are single stranded or double stranded, and the nature of the classes for which information is sought by electrophoresis.

Subsequent to electrophoretic separation, labeled polynucleotides can be detected by, for example, measuring the fluorescence emission from a dye on the labeled polynucleotides. To perform such detection, the labeled polynucleotides are illuminated by standard means, such as high intensity mercury vapor lamps, lasers, or the like. In some embodiments, the illumination means is a laser having an illumination beam at a wavelength above about 600 nm. In some embodiments, the dye-polynucleotides are illuminated by laser light generated by a He—Ne gas laser or a solid-state diode laser. After illumination, fluorescence intensity of the labeled polynucleotide can be measured by a light-sensitive detector, such as a photomultiplier tube, charged coupled device, or the like. Exemplary electrophoresis detection systems are described elsewhere, e.g., U.S. Pat. Nos. 5,543,026; 5,274,240; 4,879,012; 5,091,652 and 4,811,218.

In some embodiments, the present teachings provide for a method of fragment analysis comprising, annealing an polynucleotide primer to a denatured DNA template, such that the polynucleotide primer anneals to a complementary polynucleotide sequence on a strand of the denatured DNA template to form a primer-template complex, extending the primer portion of the primer-template complex in the presence of extendable nucleotide triphosphates and non-extendable nucleotide triphosphates to form DNA amplicon fragments and detecting the DNA amplicon fragments. In some embodiments, the polynucleotide primer can be an oligonucleotide of the present teachings. Further embodiments of fragment analysis methods in accordance with the present teachings can be found in, for example, U.S. Pat. No. 6,221,606 incorporated herein by reference.

As used herein, “ligation reaction” refers to reactions in which allele specific ligation probes are annealed to at least one DNA template strand to form a probe-template complex. After the step of annealing, a covalent bond is then formed between the probe and the second oligonucleotide fragment by a ligation agent to form a ligation product. A ligation agent according to the present invention may comprise any number of enzymatic or chemical (i.e., non-enzymatic) agents. For example, ligase is an enzymatic ligation agent that, under appropriate conditions, forms phosphodiester bonds between the 3′-OH and the 5′-phosphate of adjacent polynucleotides. Temperature-sensitive ligases, include, but are not limited to, bacteriophage T4 ligase, bacteriophage T7 ligase, and E. coli ligase. Thermostable ligases include, but are not limited to, Taq ligase, Tth ligase, and Pfu ligase. Thermostable ligase may be obtained from thermophilic or hyperthermophilic organisms, including but not limited to, prokaryotic, eucaryotic, or archael organisms. Some RNA ligases may also be employed in the methods of the invention.

Chemical ligation agents include, without limitation, activating, condensing, and reducing agents, such as carbodiimide, cyanogen bromide (BrCN), N-cyanoimidazole, imidazole, 1-methylimidazole/carbodiimide/cystamine, dithiothreitol (DTT) and ultraviolet light. Autoligation, i.e., spontaneous ligation in the absence of a ligating agent, is also within the scope of the invention. Detailed protocols for chemical ligation methods and descriptions of appropriate reactive groups can be found, among other places, in Xu et al., Nucleic Acid Res., 27:875-81 (1999); Gryaznov and Letsinger, Nucleic Acid Res. 21:1403-08 (1993); Gryaznov et al., Nucleic Acid Res. 22:2366-69 (1994); Kanaya and Yanagawa, Biochemistry 25:7423-30 (1986); Luebke and Dervan, Nucleic Acids Res. 20:3005-09 (1992); Sievers and von Kiedrowski, Nature 369:221-24 (1994); Liu and Taylor, Nucleic Acids Res. 26:3300-04 (1999); Wang and Kool, Nucleic Acids Res. 22:2326-33 (1994); Purmal et al., Nucleic Acids Res. 20:3713-19 (1992); Ashley and Kushlan, Biochemistry 30:2927-33 (1991); Chu and Orgel, Nucleic Acids Res. 16:3671-91 (1988); Sokolova et al., FEBS Letters 232:153-55 (1988); Naylor and Gilham, Biochemistry 5:2722-28 (1966); U.S. Pat. No. 5,476,930; and Royer, EP 324616B1). In some embodiments, the ligation agent is an “activating” or reducing agent. It will be appreciated that if chemical ligation is used, the 3′ end of the first probe and the 5′ end of the second probe should include appropriate reactive groups to facilitate the ligation.

In some embodiments, the present teachings provide methods of oligonucleotide ligation comprising, i) forming a complex comprising a first and a second polynucleotide strand annealed to a DNA template such that, the first polynucleotide strand anneals to a first complementary polynucleotide sequence on the strand of the denatured DNA template and the second polynucleotide strand anneals to a second complementary polynucleotide sequence on the strand of the denatured DNA template, wherein the second complementary polynucleotide sequence on the strand of the denatured DNA template is located 5′ to the first complementary polynucleotide sequence on the strand of the denatured DNA template, and ii) forming a stable covalent bond between the first and second polynucleotide strands, wherein at least one of the first polynucleotide strand or the second polynucleotide strand is a polynucleotide of the present teachings.

In some embodiments, the present teachings provide a method of oligonucleotide ligation comprising, annealing a first oligonucleotide to a strand of a denatured DNA template such that, the first oligonucleotide anneals to a complementary oligonucleotide sequence on the strand of the denatured DNA template to form a first oligonucleotide-template complex, annealing a second oligonucleotide to an oligonucleotide sequence on the first oligonucleotide-template complex that is complementary to the second oligonucleotide to form a second oligonucleotide-template complex, wherein the second oligonucleotide anneals to the first oligonucleotide-template complex so that the 3′-terminus of the first oligonucleotide and the 5′-terminus of the second oligonucleotide are associated with adjacent nucleotides of the denatured DNA template, and forming a stable covalent bond between the 3′-terminus of the first oligonucleotide and the 5′-terminus of the second oligonucleotide. In some embodiments, at least one of the first oligonucleotide or the second oligonucleotide can be an oligonucleotide of the present teachings.

In some embodiments, the present teachings provide for a method for detecting a target polynucleotide sequence comprising (a) reacting a target polynucleotide strand and a target-complementary strand with a first probe pair and a second probe pair, the first probe pair comprising (i) a first polynucleotide probe containing a sequence that is complementary to a first target region in the target strand and (ii) a second polynucleotide probe comprising a sequence that is complementary to a second target region in the target strand, wherein the second region is located 5′ to the first region and overlaps the first region by at least one nucleotide base, and the second probe pair comprising (i) a third polynucleotide probe containing a sequence that is complementary to a first region in the target-complementary strand and (ii) a fourth polynucleotide probe containing a sequence that is complementary to a second region in the target-complementary strand, wherein the second region is located 5′ to the first region and overlaps the first region by at least one nucleotide base, under conditions effective for the first and second probes to hybridize to the first and second regions in the target strand, respectively, forming a first hybridization complex, and for the third and fourth probes to hybridize to the first and second regions in the target-complementary strand, respectively, forming a second hybridization complex, (b) cleaving the second probe in the first hybridization complex, and the fourth probe in the second hybridization complex, to form (i) a third hybridization complex comprising the target strand, the first probe, and a first fragment of the second probe having a 5′ terminal nucleotide located immediately contiguous to a 3′ terminal nucleotide of the first probe, and (ii) a fourth hybridization complex comprising the target-complementary strand, the third probe, and a first fragment of the fourth probe having a 5′ terminal nucleotide located immediately contiguous to a 3′ terminal nucleotide of the third probe, (c) ligating the first probe to the hybridized fragment of the second probe to form a first ligated strand hybridized to the target strand, and ligating the third probe to the fragment of the fourth probe to form a second ligated strand hybridized to the target-complementary strand, (d) denaturing the first ligated strand from the target strand and the second ligated strand from the target-complementary strand, and (e) performing one or more additional cycles of steps (a) through (d), with the proviso that in the last cycle, step (d) is optionally omitted.

In some embodiments, the first region can overlap the second region by one nucleotide base. In some embodiments, the 5′ ends of the first and third probes can terminate with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 5′ ends of the first and third probes can terminate with a nucleotide 5′ hydroxyl group. In some embodiments, the 5′ ends of the second and fourth probes can terminate with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 5′ ends of the second and fourth probes can terminate with a nucleotide 5′ hydroxyl group. In some embodiments, the 5′ ends of the first, second, third and fourth probes can each independently terminate with a group other than a nucleotide 5′ phosphate group. In some embodiments, the 3′ ends of the second and fourth probes can each independently terminate with a group other than a nucleotide 3′ hydroxyl group. In some embodiments, the 3′ ends of the second and fourth probes can terminate with a nucleotide 3′ phosphate group.

In some embodiments, at least one of the probes can contain a detectable label. In some embodiments, the label can be a fluorescent label. In some embodiments, the label can be a radiolabel. In some embodiments, the label can be a chemiluminescent label. In some embodiments, the label can be an enzyme. In some embodiments, at least one of the first probe and the third probe can contain a detectable label. In some embodiments, each of the first probe and third probe can contain a detectable label. In some embodiments, the detectable labels on the first probe and third probe can be the same. In some embodiments, at least one of the second probe and the fourth probe can contain a detectable label. In some embodiments, each of the second probe and the fourth probe contains a detectable label. In some embodiments, the second probe and fourth probe can contain the same detectable label.

In some embodiments, the step of cleaving produces a second fragment from the second probe which does not associate with the third hybridization complex, and the method further includes detecting said second fragment.

In some embodiments, at least one of the second probe and the fourth probe contains both (i) a fluorescent dye and (ii) a quencher dye which is capable of quenching fluorescence emission from the fluorescent dye when the fluorescent dye is subjected to fluorescence excitation energy, and said cleaving severs a covalent linkage between the fluorescent dye and the quencher dye in the second probe and/or fourth probe, thereby increasing an observable fluorescence signal from the fluorescent dye. In some embodiments, the second probe and the fourth probe can each contain (i) a fluorescent dye and (ii) a quencher dye.

In some embodiments, the step of cleaving further produces a second fragment from the fourth probe that does not associate with the fourth hybridization complex, and the method further includes detecting both second fragments. In some embodiments, the second fragment comprises one or more contiguous nucleotides that are substantially non-complementary to the target strand. In some embodiments, one or more contiguous nucleotides comprise 1 to 20 nucleotides.

In some embodiments, the method further includes immobilizing the second fragment on a solid support. In some embodiments, the method further includes subjecting the second fragment to electrophoresis. In some embodiments, the method further includes detecting the second fragment by mass spectrometry. In some embodiments, the method further comprises detecting the second fragment after the last cycle. In some embodiments, the method further comprises detecting the second fragment during or after a plurality of cycles. In some embodiments, the method further comprises detecting the second fragment during all of the cycles. In some embodiments, the method further includes detecting the first hybridization complex, the second hybridization complex, or both, after at least one cycle. In some embodiments, the method further includes detecting the third hybridization complex, the fourth hybridization complex, or both, after at least one cycle. In some embodiments, the method further includes detecting the first ligated strand, the second ligated strand, or both, after at least one cycle. In some embodiments, said detecting comprises an electrophoretic separation step.

Further embodiments of the ligation method for detecting a target polynucleotide can be found in Bi, W., et al., U.S. Pat. No. 6,511,810 incorporated herein by reference in its entirety.

EXAMPLES Materials and Methods

Unless otherwise indicated, all synthesis reactions were carried out in oven or flame dried glassware, under an atmosphere of argon. Tetrahydrofuran (THF) and methylene chloride (CH₂Cl₂) were distilled from calcium hydride (CaH₂) under Argon. Unless otherwise indicated, all other solvents were used as received from the distributor. Thin layer chromatography (TLC) was performed on 1 mm silica gel plates purchased from Sigma-Aldrich (Milwaukee, Wis.) and visualized with UV light (Spectroline; model ENF-240C) or stained with KMnO₄ or phosphomolybdic acid. Flash column chromatography was performed using silica gel with an average particle size of 40 μm purchased from Sigma-Aldrich (Milwaukee, Wis.). 8-Aza-7-deaza-2′-deoxyguanine was purchased from EPOCH Biosciences Inc (Bothell, Wash.). 8-Aza-7-deaza-2′-deoxyadenosine was purchased from Berry & Associates Inc (Dexter, Mich.). Non-derivatized CPG support was obtained from Applied Biosystems Inc (P/N 360139, Foster City, Calif.). Unless otherwise indicated, all other reagents were purchased from Sigma-Aldrich. Unless otherwise indicated, automated DNA synthesis was carried out on an ABI 394 DNA synthesizer at a 0.2 μmol scale following the standard protocol. Oligonucleotides were purified by reversed phase HPLC on an Agilent 1100 HPLC system. ESI-TOF mass spectra were recorded on a MARINER® Biospectrometry Workstation (Applied Biosystems, Foster City). The purity of synthesized oligo-nucleotides was checked by capillary electrophoresis (CE) on an Agilent CE system.

Oligonucleotide Synthesis 8-Aza-7-deaza-2′-deoxyadenosine CPG

8-Aza-7-deaza-2′-deoxyadenosine CPG was prepared according to Scheme 3.

N-Benzoyl-5′-dimethoxytrityl-2′-deoxyadenosine

To a stirred solution of 50 mg of 8-aza-7-deaza-2′-deoxyadenosine in 1 mL of dry pyridine was added 100 mg of DMT-Cl, 42 μL Et₃N and 600 μg DMAP. The reaction was stirred at room temperature for 4 hours and then 128 μL of trimethylsilyl chloride (TMS-Cl) was added. The reaction was then stirred for an additional 30 minutes at room temperature at which time 116 μL of benzoyl chloride (BzCl) was added and the mixture stirred for an additional 2 hours. The mixture was then cooled to 0° C. in an ice bath and 200 μL of water was added. After stifling for 5 minutes, 400 μL of 29% aqueous ammonia was added and the mixture was stirred at room temperature for 30 minutes. The solvent was evaporated and the residue was partitioned between 3 mL of CH₂Cl₂ and 3 mL of 5% aqueous NaHCO₃. The layers were separated and organic layer was evaporated to dryness. The crude product was purified by silica gel chromatography (12.5/1 CH₂Cl₂/MeOH) to give 16 mg of the desired product (12% yield).

N-Benzoyl-3′-(3-carboxypropionyl)-5′-dimethoxytrityl-2′-deoxyadenosine

To a stirred solution of 16 mg of N-benzoyl-5′-dimethoxytrityl-2′-deoxy-adenosine in 2 mL of CH₂Cl₂ was added 4.3 mg succinic anhydride, 1.5 mg DMAP and 7.2 μL Et₃N. The reaction was stirred at room temperature for 12 hours at which time the reaction was diluted with 10 mL of 5% aqueous citric acid. The organic layer was washed with sat. NaCl, dried over anhydrous Na₂SO₄ and the solvent removed under vacuum. The crude product was purified by silica gel chromatography (100/50/1 CH₂Cl₂/MeOH/Et₃N) to give 12 mg of the desired product.

8-Aza-7-deaza-2′-deoxyadenosine CPG

To a solution of 12 mg N-benzoyl-3′-(3-carboxypropionyl)-5′-dimethoxytrityl-2′-deoxyadenosine in 1 mL of dry DMF was added 3.6 μL DIPEA, 5.3 mg of HBTU and 300 mg of CPG. The mixture was stirred for 2 hours at room temperature and then washed with DMF followed by THF. The 8-Aza-7-deaza-2′-deoxyadenosine CPG product was dried under high vacuum.

N2-(N,N-Dimethylformamido-3′-(3-carboxypropionyl)-5′-dimethoxytrityl-8-aza-7-deaza-2′-deoxyguanosine

To a stirred solution of N2-(N,N-Dimethylformamido-5′-dimethoxytrityl-8-aza-7-deaza-2′-deoxyguanosine (e.g., see Seela et al., Helv. Chem. Acta (1986) 69:1602-1613; (1988) 71:1191-1198) in 10 mL of dry CH₂Cl₂ was added 140 mg succinic anhydride, 210 μL Et₃N, and 62 mg of DMAP. The reaction was stirred at room temperature for 4 hours and then diluted with 20 mL of CH₂Cl₂ and washed with 5% aqueous citric acid solution (2×20 mL) and saturated NaCl (1×20 mL). The organic layer was dried over anhydrous Na₂SO₄ and evaporated to give 850 mg of the desired product as a colorless foam (in Scheme 4 below, Ndmf represents N,N-dimethylformamidino).

8-Aza-7-deaza-2′-deoxyguanisine CPG

8-Aza-7-deaza-2′-deoxyguanisine CPG was prepared according to Scheme 4 below.

To a stirred solution of N2-(N,N-Dimethylformamido-3′-(3-carboxypropionyl)-5′-dimethoxytrityl-8-aza-7-deaza-2′-deoxyguanosine in 10 mL of dry DMF was added 117 μL of DIPEA, 86 mg of HBTU, and 5 g of CPG. The mixture was stirred for 4 hours at room temperature and then washed with DMF, CH₃CN and CH₂Cl₂. The 8-aza-7-deaza-2′-deoxyguanosine CPG product was dried under high vacuum.

3′-Terminal oligonucleotides of 8-aza-7-deaza-2′-deoxyguanosine and 8-aza-7-deaza-2′-deoxyadenosine

As mentioned above, automated DNA synthesis was carried out on an ABI 394 DNA synthesizer at a 0.2 μmol scale following the standard protocol. Oligonucleotides were purified by reversed phase HPLC on an Agilent 1100 HPLC system. To that end, the oligonucleotides shown in Tables 1-2 were synthesized. Forward primer AGTFcA and reverse primer AGTRcA amplify part of the human angiotesinogen gene (AGT, ˜100 bp). Forward primer ATIRFcA and reverse primer ATIRRcA amplify part of the angiotensin II type 1 receptor gene (ATIR, ˜100 bp). Forward primer AGTFcG and reverse primer AGTRcG amplify part of the human angiotesinogen gene (AGT, 75 bp). Forward primer ATIRFcG and reverse primer ATIRRcG amplify part of the angiotensin II type 1 receptor gene (ATIR, 200 bp).

TABLE 1 Primers Primer Sequences X = A X = ppA (5′ → 3′ = left to right) AGTFcA AGTFcA-ppA CACCCTCATGGCCTCATTTTX AGTRcA AGTRcA-ppA AATGCCCGTGTTGAAGTCCTAX ATIRFcA ATIRFcA-ppA GTGTTTCTACTCACGTGTCTCAGCX ATIRRcA ATIRRcA-ppA TGCAGGTGACTTTGGCTACAX

TABLE 2 Primers X = G X = ppG Primer Sequences AGTFcG AGTFcG-ppG GCAAAATGATATTTCAGGTATGCGX AGTRcG AGTRcG-ppG CCCTCAGGCTCACACCGX ATIRFcG ATIRFcG-ppG GCTCATCCACCAAGAAGCCTX ATIRRcG ATIRRcG-ppG TTTGTTCAGAGCTTTAGAAAAGTCGX

8-Aza-7-deaza-2′-deoxyguanosine containing oligonucleotides

As mentioned above, automated DNA synthesis was carried out on an ABI 394 DNA synthesizer at a 0.2 μmol scale following the standard protocol. Oligonucleotides were purified by reversed phase HPLC on an Agilent 1100 HPLC system. oligonucleotides shown in Table 3 were synthesized using 8-aza-7-deaza-2′-deoxyguanosine phosphoramidite to incorporate 8-aza-7-deaza-2′-deoxyguanosine at positions other than the 3′ terminus. 8-Aza-7-deaza-2′-deoxyguanosine phosphoramidite was prepared according to Seela, F., et al., Helvetica Chimica Acta, v. 71, 1191-1198 (1988). Forward primer Lamda-FcG and reverse primer Lamda-RcG amplify a 1700 bp target of λ-DNA.

TABLE 3 Primers X = G X = ppG Primer Sequences Lamda-FcG Lamda-FcG-ppG ATCAGAAACGAACGCATCATCAAXT Lamda-RcG Lamda-RcG-ppG AAACAGCCACAAAGCCAGCCGXAAT

Amplifications:

gDNA amplifications were carried out with 5000 copies of gDNA per 15 μL reaction and X-DNA amplifications were carried out with 1500 copies of gDNA per 15 μL reaction.

Amplifications were carried out using either unmodified and/or modified primers in 15 μL reactions containing the following reagents

-   -   10 mM Tris-HCl buffer, pH 8.3     -   50 mM KCl, 3 mM MgCl₂, 0.01% v/v gelatin     -   0.2 mM dATP, 0.2 mM dCTP, 0.2 mM dGTP, and 0.4 mM dUTP     -   0.025 unit/pt AmpliTaq Gold° DNA polymerase (Applied Biosystems,         P/N N808-0107)     -   200 nM of each forward and reverse primer     -   water for no template control (NTC) experiments or 15 ng genomic         DNA (Applied Biosystems, P/N 403062)

The progress of all PCR reactions was monitored in real time on an ABI PRISM® 7900HT Sequence Detection System (Applied Biosystems; Foster City, Calif.) as described in SYBR® Green PCR Master Mix and RT-PCR: Protocol (Applied Biosystems, 2002).

Thermal Cycling:

Thermal Cycling Protocol #1:

Amplification temperature cycling was carried out using the following thermal cycling protocol.

TABLE 4 AmpliTaq Gold ® 50 Cycles Activation Denature Anneal/Extend Temperature (° C.) 95 95 60 72 Time 2 min 15 sec 30 sec 30 sec

Thermal Cycling Protocol #2:

Amplification temperature cycling was carried out using the following thermal cycling protocol.

TABLE 5 AmpliTaq Gold ® 50 Cycles Activation Denature Anneal/Extend Temperature (° C.) 95 95 55 72 Time 2 min 15 sec 30 sec 30 sec

Thermal Cycling Protocol #3:

Amplification temperature cycling was carried out using the following thermal cycling protocol.

TABLE 6 AmpliTaq Gold ® 50 Cycles Activation Denature Anneal/Extend Temperature (° C.) 93 93 60 72 Time 2 min 60 sec 50 sec 90 sec

Amplification Reaction Analysis:

All amplification products were analyzed by gel electrophoresis as follows. PCR reaction mixture (15 μL) was diluted with 5 μL nuclease-free water. This solution was loaded along with 25 bp DNA ladder into wells of 4% agarose gel (Invitrogen, P/N G5018-04). Electrophoresis was carried out at 12 V DC at 880 mA for 30 minutes. Ethidium bromide stained bands of dsDNA were visualized using UV irradiation and quantified by AlphaDigDoc 1000 software (Alpha Innotech; San Leandro, Calif.) equipped with a Kodak digital camera.

Amplifications Using 3′-Terminus Modified Primers:

2′-deoxy-PPA 3′-Terminal Primers

Amplification reactions using 2′-deoxy-PPA 3′-terminal primers, shown in Table 1, were carried out according to Thermal Cycling Protocol #2.

For each primer pair, amplification reactions using unmodified and 3′-modified primers were run with gDNA corresponding to the primer pair. Additionally, amplification reactions were also run without any template as no template control (NTC) reactions.

Gel electrophoresis analysis was carried out as described above. Gel electrophoresis showed a significant amount of non-specific amplification product at about 50 bp in NTC amplifications with unmodified primers indicating the formation of primer-dimer amplicons. On the other hand, decreased primer-dimer amplicon formation was observed in gel electrophoresis images of NTC amplifications using 3′-modified primers. Gel electrophoresis of gDNA template amplification reactions using unmodified primers clearly showed a band corresponding to the desired template amplicon and also showed a band at corresponding to primer-dimer amplicon formation.

Amplification of AGT template using unmodified primers clearly showed a band at about 75 bp corresponding to the desired template amplicon and also showed a band at about 50 bp corresponding to primer-dimer amplicon formation. On the other hand, amplification of AGT template using 3′-modified primers clearly showed a band at about 75 bp corresponding to the desired template amplicon but also showed no primer-dimer amplicon formation.

Real time PCR monitoring showed that the gDNA amplification efficiencies using unmodified- and 3′-modified-primers were very similar. On the other hand, while the NTC amplification using unmodified primers gave a C_(t) value, which is the calculated cycle number at which detectable signal rises above background, of about 28, NTC amplification using ppA modified primers did not give a measurable signal until about the 33^(rd) cycle.

Amplification of ATIR template using unmodified primers clearly showed a band at about 200 bp corresponding to the desired template amplicon and also showed a band at about 50 bp corresponding to primer-dimer amplicon formation. On the other hand, amplification of ATIR template using 3′-modified primers clearly showed a band at about 200 bp corresponding to the desired template amplicon but also showed no primer-dimer amplicon formation.

Real time PCR monitoring showed that the gDNA amplification efficiencies using unmodified- and 3′-modified-primers were good. NTC amplification using unmodified primers gave a C_(t) value of about 33, whereas NTC amplification using ppA modified primers did not give a measurable signal until about the 42^(nd) cycle.

2′-deoxy-PPG 3′-Terminal Primers

Amplification reactions using 2′-deoxy-PPG 3′-terminal primers, shown in Table 2, were carried out according to Thermal Cycling Protocol #1.

For each primer pair, amplification reactions using unmodified and 3′-modified primers were run with gDNA corresponding to the primer pair. Additionally, amplification reactions using unmodified and 3′-modified primers were run without any template as no template control (NTC) reactions.

Gel electrophoresis analysis was carried out as described above. Gel electrophoresis showed a significant amount of non-specific amplification product at about 50 bp in NTC amplifications with unmodified primers indicating the formation of primer-dimer amplicons. On the other hand, significantly decreased primer-dimer amplicon formation was observed in gel electrophoresis images of NTC amplifications using 3′-modified primers. Gel electrophoresis of gDNA template amplification reactions using unmodified primers clearly showed a band corresponding to the desired template amplicon and also showed a band at corresponding to primer-dimer amplicon formation.

Amplification of AGT template using unmodified primers clearly showed a band at about 75 bp corresponding to the desired template amplicon and also showed a band at about 50 bp corresponding to primer-dimer amplicon formation. On the other hand, amplification of AGT template using 3′-modified primers clearly showed a band at about 75 bp corresponding to the desired template amplicon but also showed no primer-dimer amplicon formation.

Real time PCR monitoring showed that the gDNA amplification efficiencies using unmodified- and 3′-modified-primers were very similar. On the other hand, while the NTC amplification using unmodified primers gave a C_(t) value of about 23, a value which was almost equivalent to the gDNA amplifications, NTC amplification using ppG modified primers did not give a measurable signal until after the 33^(rd) cycle.

Amplification of ATIR template using unmodified primers clearly showed a band at about 200 bp corresponding to the desired template amplicon and also showed a band at about 50 bp corresponding to primer-dimer amplicon formation. On the other hand, amplification of ATIR template using 3′-modified primers clearly showed a band at about 200 bp corresponding to the desired template amplicon but also showed no primer-dimer amplicon formation.

Real time PCR monitoring showed that the gDNA amplification efficiencies using unmodified- and 3′-modified-primers were similar. On the other hand, while the NTC amplification using unmodified primers gave a C_(t) value of about 22, NTC amplification using ppG modified primers did not give a measurable signal until about the 30^(th) cycle.

λ-DNA Amplifications:

To test whether 3′-modified primers of the present teachings could reduce non-specific amplification without effecting amplification efficiency of longer amplicons, λ-DNA was used as a template with primers designed to make a 1700 bp target amplicon.

2′-Deoxy-PPG λ-DNA Amplification:

Amplification reactions using 2′-deoxy-PPG containing primers, shown in Table 3, were carried out according to Thermal Cycling Protocol #3. As above, both real time analysis and gel electrophoresis showed that even with longer amplicons, 3′-modification with 2′-deoxy-PPG resulted in significant reduction in primer-dimer amplification without adversely effecting target amplification efficiency. Amplification efficiencies of λ-DNA template using both unmodified and modified primers were nearly identical, C_(t) about 24. NTC amplification using unmodified primers gave a C_(t) value of about 32, whereas NTC amplification using 2′-deoxy-PPG modified primers gave no detectable signal until after the 42^(nd) cycle. 

1-98. (canceled)
 99. A method of DNA amplicon fragment analysis comprising: i) annealing an oligonucleotide primer to a denatured DNA template such that, the oligonucleotide primer anneals to a complementary oligonucleotide sequence on a strand of the denatured DNA template to form a primer-template complex, wherein the oligonucleotide primer comprises at least one modified purine nucleobase comprising the structure:

wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, azido, nitro, cyano, unsubstituted or substituted amino, C₁-C₆ alkyl, C₁-C₆ alkynyl, C₁-C₆ substituted alkynyl, unsubstituted or substituted phenylalkynyl, and unsubstituted or substituted aryl; at least one said modified purine nucleobase is no more than 3 nucleotides from the 3′ terminus of the oligonucleotide primer; and the oligonucleotide primer is extendable at its 3′-end; ii) extending the primer portion of the primer-template complex in the presence of extendable nucleotide triphosphates and non-extendable nucleotide triphosphates to form one or more DNA amplicon fragments; and iii) detecting the DNA amplicon fragments.
 100. The method of claim 99, wherein the at least one modified purine nucleobase is no more than 2 nucleotides from the 3′ terminus of the oligonucleotide primer.
 101. The method of claim 99, wherein the at least one modified purine nucleobase is no more than 1 nucleotides from the 3′ terminus of the oligonucleotide primer.
 102. The method of claim 99, wherein the at least one modified purine nucleobase is the 3′ terminal nucleotide of the oligonucleotide primer.
 103. The method of claim 99, wherein detecting the amplicon DNA fragments comprises a size-dependent separation process to generate separated DNA amplicon fragments.
 104. The method of claim 103 wherein the size dependent separation process may comprise electrophoresis, chromatography or combinations thereof.
 105. The method of claim 99, wherein the oligonucleotide primer further comprises at least one of a detectable label, a quencher or a minor groove binder, or any combination thereof.
 106. The method of claim 105, comprising generating labeled DNA amplicon fragments.
 107. The method of claim 106 further comprising detecting the DNA amplicon fragments by laser-induced fluorescence.
 108. The method of claim 105, comprising using a plurality of labeled oligonucleotide primers wherein each labeled oligonucleotide primer is labeled with a different and spectrally resolvable label.
 109. The method of claim 108, wherein the DNA amplicon fragments are formed using chain termination methods of DNA sequencing.
 110. The method of claim 109 wherein the DNA amplicon fragments may be identified by identifying terminal nucleotides in each of the DNA amplicon fragment and wherein a correspondence is established between the four possible terminal nucleotides and a set of spectrally resolvable labels.
 111. The method of claim 99, wherein the oligonucleotide primer comprising the at least one said modified purine nucleobase comprises the structure:


112. The method of claim 99, wherein the oligonucleotide primer comprising the at least one said modified purine nucleobase comprises the structure:


113. The method of claim 99, wherein the oligonucleotide primer comprising the at least one said modified purine nucleobase comprises the structure:


114. A method of DNA amplicon fragment analysis comprising: i) annealing an oligonucleotide primer to a denatured DNA template such that, the oligonucleotide primer anneals to a complementary oligonucleotide sequence on a strand of the denatured DNA template to form a primer-template complex, wherein the oligonucleotide primer comprises at least one modified purine nucleobase comprising the structure:

wherein R₁ is selected from hydrogen, halogen, fluorine, chlorine, bromine, iodine, azido, nitro, cyano, unsubstituted or substituted amino, C₁-C₆ alkyl, C₁-C₆ alkynyl, C₁-C₆ substituted alkynyl, unsubstituted or substituted phenylalkynyl, and unsubstituted or substituted aryl; at least one said modified purine nucleobase is no more than 3 nucleotides from the 3′ terminus of the oligonucleotide primer, and the oligonucleotide primer is extendable at its 3′-end; ii) extending the primer portion of the primer-template complex in the presence of deoxyribonucleic acids and non-extendable ribonucleic acids to form one or more DNA amplicon fragments; and iii) detecting the DNA amplicon fragments.
 115. The method of claim 114, wherein the oligonucleotide primer comprising the at least one said modified purine nucleobase comprises the structure:


116. The method of claim 114, wherein the oligonucleotide primer comprising the at least one said modified purine nucleobase comprises the structure:


117. The method of claim 114, wherein the oligonucleotide primer comprising the at least one said modified purine nucleobase comprises the structure: 